ArticleJournal of chemical information and modeling2018
Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.
Article in Journal of chemical information and modeling, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- MEGPNM as a multiscale edge-aware GAT network with hybrid pooling predicting permeability of non-peptidic macrocycles.Communications chemistry · 2026Article
- Comparative molecular dynamics of two cyclic peptide inhibitors bound to the Zika virus NS2B/NS3 protease.Journal of molecular modeling · 2026Article
- Toward the Engineering of Chameleonicity: Quantum Mechanical Prediction for the Octanol/Water Distributions of Large Flexible Triazine Macrocycles.Journal of chemical information and modeling · 2026Article
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- Article
- Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.bioRxiv : the preprint server for biology · 2025Article
- Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents.Journal of chemical information and modeling · 2024Article
- Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.PloS one · 2024Article
- Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.Journal of chemical information and modeling · 2023Article
- pyPept: a python library to generate atomistic 2D and 3D representations of peptides.Journal of cheminformatics · 2023Article
- A Model for the Rapid Assessment of Solution Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation.The Journal of organic chemistry · 2023Article
- Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst.ChemCatChem · 2022Article
- A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo.Nature communications · 2022Article
- Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution.ACS omega · 2022Article
- Navigating complex peptide structures using macrocycle conformational maps.RSC chemical biology · 2022Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis.Topics in catalysis · 2022Article
- Peptide stapling by late-stage Suzuki-Miyaura cross-coupling.Beilstein journal of organic chemistry · 2022Article
- Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Energy penalties enhance flexible receptor docking in a model cavity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering, we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides. The resulting structural and thermodynamic information is benchmarked against interproton distances from NMR experiments and conformational states identified by X-ray crystallography. Using three different model systems of varying size and flexibility, we show that the method reliably reproduces experimentally determined structural ensembles and is capable of identifying key conformational states that include the bioactive conformation. Thus, the described approach is a robust method to generate conformations of peptidic macrocycles and holds promise for structure-based drug design.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.